/*
FILE:     connect_util.C
*/
/*
VERSION:  1.600
*/
/*
DATE:     2/3/2005
*/
/*
  Comments and Questions to: sw-help@rcsb.rutgers.edu
*/
/*
COPYRIGHT 1999-2005 Rutgers - The State University of New Jersey

This software is provided WITHOUT WARRANTY OF MERCHANTABILITY OR
FITNESS FOR A PARTICULAR PURPOSE OR ANY OTHER WARRANTY, EXPRESS OR
IMPLIED.  RUTGERS MAKE NO REPRESENTATION OR WARRANTY THAT THE
SOFTWARE WILL NOT INFRINGE ANY PATENT, COPYRIGHT OR OTHER
PROPRIETARY RIGHT.

The user of this software shall indemnify, hold harmless and defend
Rutgers, its governors, trustees, officers, employees, students,
agents and the authors against any and all claims, suits,
losses, liabilities, damages, costs, fees, and expenses including
reasonable attorneys' fees resulting from or arising out of the
use of this software.  This indemnification shall include, but is
not limited to, any and all claims alleging products liability.
*/
/*
               PDB SOFTWARE LICENSE AGREEMENT

BY CLICKING THE ACCEPTANCE BUTTON OR INSTALLING OR USING 
THIS "SOFTWARE, THE INDIVIDUAL OR ENTITY LICENSING THE  
SOFTWARE ("LICENSEE") IS CONSENTING TO BE BOUND BY AND IS 
BECOMING A PARTY TO THIS AGREEMENT.  IF LICENSEE DOES NOT 
AGREE TO ALL OF THE TERMS OF THIS AGREEMENT
THE LICENSEE MUST NOT INSTALL OR USE THE SOFTWARE.

1. LICENSE AGREEMENT

This is a license between you ("Licensee") and the Protein Data Bank (PDB) 
at Rutgers, The State University of New Jersey (hereafter referred to 
as "RUTGERS").   The software is owned by RUTGERS and protected by 
copyright laws, and some elements are protected by laws governing 
trademarks, trade dress and trade secrets, and may be protected by 
patent laws. 

2. LICENSE GRANT

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The license granted under this Agreement gives Licensee no rights to such
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7. DISCLAIMER OF WARRANTY.  THE SOFTWARE IS PROVIDED FREE OF 
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THIS DISCLAIMER OF WARRANTY CONSTITUTES AN ESSENTIAL PART OF 
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8. LIMITATION OF LIABILITY.  TO THE MAXIMUM EXTENT PERMITTED BY
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INDIRECT, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING 
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*/
#include <stdio.h>
#include <string.h>
#include <sys/stat.h>

#include "connect_check.h"
#include "connect_iolib.h"
#include "connect_util.h"
#include "connect2graph.h"
#include "erf_util.h"
#include "ndb_misclib.h"

static void waiting_for_continue();
static char *Get_words(char *string, char *buffer, const char begin, const char end);
static void Write_PDB_Conect_File(FILE *fp, ConnectFormat *drug);
static void print_atom_atomName_field(char *temp_line, const char *atomName, const int align);
static char *get_max_length_word(char *string, char *words, const int max_length);

void Add_Classification(Connect_Adm *Dictionary, const char *filename)
{
       FILE *fp = fopen(filename, "r");
       if (fp == NULL) {
            printf("Can't open file %s\n", filename);
            return;
       }

       char line[1000], id[5], class_1[200], class_2[200], date[20], *p = NULL;
       ConnectFormat *drug = NULL;
       while (!feof(fp)) {
            fgets(line, 999, fp);
            if (feof(fp)) break;
            p = Get_words(line, id, '\'', '\'');
            p = Get_words(p, class_1, '\'', '\'');
            p = Get_words(p, class_2, '\'', '\'');
            ndb_clean_string(id);
            ndb_set_string_to_upper(id);
            ndb_clean_string(class_1);
            ndb_set_string_to_upper(class_1);
            ndb_clean_string(class_2);
            ndb_set_string_to_upper(class_2);
            drug = Dictionary->find_drug(id);
            if (drug == NULL) continue;
            get_date(date);
            drug->set_class_1(class_1);
            drug->set_class_2(class_2);
            drug->set_modified_date(date);
       }
       fclose (fp);
       Dictionary->WriteNdbConnect("conect_new.cif");
       Dictionary->WriteChemComp("component_new.cif", 0, "");
}

void Add_Component_to_Dictionary(Connect_Adm *Dictionary)
{
       int num = 0, n, i, ret, n_list, found;
       char filename[80], date[30], value[10], *diags = NULL, **blockName = NULL;
       BTreeObj<_SSIndex> Index;
       CifFileObj *fobjR = NULL;
       CifString string, string1;
       ConnectFormat **drug = NULL, *drug_tmp = NULL;
       DiGraph *graph = NULL, *graph1 = NULL;
       _MATCH_LIST *list = NULL;
       _SSIndex _ssidx;
       struct stat stat1;

       memset(filename, 0, 80);
       system("clear");
       printf("\nEnter Het Group file name -->  ");
       fflush(stdout);
       fflush(stdin);
       fscanf(stdin, "%s", filename);
       ndb_clean_string(filename);

       if (stat(filename, &stat1) < 0) {
            printf("Can not find file: %s\n", filename);
            waiting_for_continue();
            return;
       }

       fobjR = new CifFileObj("TEMP.CIF", WRITE_MODE);
       if (fobjR == NULL) {
            printf("Import Het Group(s) %s into component.cif failed\n", filename);
            waiting_for_continue();
            return;
       }

       fobjR->Read(filename, diags);
       if (diags && strlen(diags)) {
            printf("Read cif file %s failed\n%s\n", filename, diags);
            waiting_for_continue();
            if (fobjR) delete fobjR;
            return;
       }

       Index.Clear();
       drug_tmp = Dictionary->GetFirstConnect();
       while (drug_tmp) {
            string.Copy("");
            if (drug_tmp->formula() && strcmp(drug_tmp->formula(), ""))
                 string.Copy(drug_tmp->formula());
            ReorderFormula(string, string1, 0);
            _ssidx.set_ivalue(drug_tmp->drugname());
            _ssidx.set_svalue(string.Text());
            Index.Add(_ssidx);
            drug_tmp = Dictionary->GetNextConnect();
       }

       blockName = fobjR->GetBlockNames(num);
       drug = new ConnectFormat*[num];
       for (i = 0; i < num; i++) drug[i] = NULL;

       found = 0;
       get_date(date);
       for (n = 0; n < num; n++) {
            drug[n] = new ConnectFormat();
            if (Read_Chem_Comp(drug[n], fobjR, blockName[n], 1)) {
                 printf("Read Het Group %s failed\n", blockName[n]);
                 waiting_for_continue();
                 for (i = 0; i < num; i++) {
                      delete [] blockName[i];
                      if (drug[i]) delete drug[i];
                 }
                 delete [] blockName;
                 delete [] drug;
                 if (fobjR) delete fobjR;
                 return;
            }

            if (drug[n]->formal_charge() && strcmp(drug[n]->formal_charge(), "") &&
                strcmp(drug[n]->formal_charge(), "0")) {
                 strcpy(value, drug[n]->formal_charge());
                 reformatting_charge_to_suffix(value);
                 drug[n]->set_formal_charge(value);
            }
            drug[n]->set_modified_date(date);

            if (CheckFormula(drug[n], stdout, string) ||
               !CheckConnect(drug[n], stdout, string)) {
/*
                 waiting_for_continue();
                 for (i = 0; i < num; i++) {
                      delete [] blockName[i];
                      if (drug[i]) delete drug[i];
                 }
                 delete [] blockName;
                 delete [] drug;
                 if (fobjR) delete fobjR;
                 return;
*/
                 found |= 2;
            }

            if (!strcasecmp(drug[n]->drugname(), "UNL")) {
                 found |= 1;
                 printf("Het Group ID 'UNL' is reserved for 'unknown ligand'.\n");
                 printf("Please change to another ID.\n");
            }

            if (drug[n]->FindAlignPos()) {
                 found |= 1;
                 printf("%s: rcsb_align error\n", drug[n]->drugname()); 
            }

            drug_tmp = Dictionary->find_drug(drug[n]->drugname());
            if (drug_tmp) {
                 found |= 1;
                 printf("%s exists: New [%s (%s)] --- Old [%s (%s)]\n", drug[n]->drugname(),
                        drug[n]->chemical_name(), drug[n]->formula(),
                        drug_tmp->chemical_name(), drug_tmp->formula());
            }

            graph = Connect2Graph(drug[n]);
            if (graph) {
                 string.Copy(drug[n]->formula());
                 ReorderFormula(string, string1, 0);
                 _ssidx.set_svalue(string.Text());
                 ret = Index.Seek(_ssidx);
                 while (ret >= 0) {
                      _ssidx = Index.GetCurrData();
                      drug_tmp = Dictionary->find_drug(_ssidx.ivalue());
                      graph1 = Connect2Graph(drug_tmp);
                      if (graph1) {
                           list = graph1->find_match(*graph, n_list);
                           if (list && n_list == drug[n]->natoms() &&
                               n_list == drug_tmp->natoms()) {
                                printf("%s is an EXACT MATCH for %s\n",
                                    drug[n]->drugname(), drug_tmp->drugname());
                                found |= 1;
                           }
                           if (list) delete [] list;
                           delete graph1;
                      }
                      ret = Index.GoToNext();
                      if (ret >= 0 && Index.GetCurrData() != _ssidx) break;
                 }
                 delete graph;
            }
       }
       for (i = 0; i < num; i++) delete [] blockName[i];
       delete [] blockName;

       if (found & 2) {
            waiting_for_continue();
            for (i = 0; i < num; i++) {
                 if (drug[i]) delete drug[i];
            }
            delete [] drug;
            if (fobjR) delete fobjR;
            return;
       } else if (found) {
            strcpy(filename, "no");
            printf("\n\n Do you want to continue ? (yes/no) : ");
            fflush(stdout);
            fflush(stdin);
            fscanf(stdin, "%s", filename);
            if (filename[0] == 'n' || filename[0] == 'N') {
                 for (i = 0; i < num; i++) {
                      if (drug[i]) delete drug[i];
                 }
                 delete [] drug;
                 if (fobjR) delete fobjR;
                 return;
            }
       } else waiting_for_continue();

       for (i = 0; i < num; i++) {
            // drug[i]->FindAlignPos();
            drug[i]->ReorderAtoms();
            drug_tmp = Dictionary->find_drug(drug[i]->drugname());
            if (drug_tmp) {
                 if (drug_tmp->type() && strcmp(drug_tmp->type(), "NON-POLYMER") &&
                    (!drug[i]->type() || drug[i]->type() &&
                     !strcmp(drug[i]->type() , "NON-POLYMER")))
                      drug[i]->set_type(drug_tmp->type());

                 if (drug_tmp->AtomType() && strcmp(drug_tmp->AtomType(), "HETAIN") &&
                    (!drug[i]->AtomType() || drug[i]->AtomType() &&
                     !strcmp(drug[i]->AtomType() , "HETAIN")))
                      drug[i]->set_AtomType(drug_tmp->AtomType());

                 if (drug_tmp->typeModified() != 0 && drug[i]->typeModified() == 0)
                      drug[i]->set_typeModified(drug_tmp->typeModified());

                 if (drug_tmp->class_1() && strcmp(drug_tmp->class_1(), "") &&
                    (!drug[i]->class_1() || drug[i]->class_1() &&
                     !strcmp(drug[i]->class_1() , "")))
                      drug[i]->set_class_1(drug_tmp->class_1());

                 if (drug_tmp->class_2() && strcmp(drug_tmp->class_2(), "") &&
                    (!drug[i]->class_2() || drug[i]->class_2() &&
                     !strcmp(drug[i]->class_2() , "")))
                      drug[i]->set_class_2(drug_tmp->class_2());

                 if (drug_tmp->het_name() && strcmp(drug_tmp->het_name(), "") &&
                    (!drug[i]->het_name() || drug[i]->het_name() &&
                     !strcmp(drug[i]->het_name() , "")))
                      drug[i]->set_het_name(drug_tmp->het_name());

                 if (drug_tmp->status() && !strcmp(drug_tmp->status(), "REL") &&
                    (!drug[i]->status() || drug[i]->status() &&
                     strcmp(drug[i]->status() , "REL")))
                      drug[i]->set_status(drug_tmp->status());
            }
            Dictionary->add_drug(drug[i]);
       }
       delete [] drug;

       delete fobjR;

       Dictionary->WriteNdbConnect("conect_new.cif");
       Dictionary->WriteChemComp("component_new.cif", 0, "");
}

void Compare_Component_with_Dictionary(Connect_Adm *Dictionary)
{
       int i, n, num = 0, n_list, found;
       char filename[80], *diags = NULL, **blockName = NULL;
       CifFileObj *fobjR = NULL;
       CifString string, string1, string2;
       ConnectFormat **drug = NULL, *drug_tmp = NULL;
       DiGraph *graph = NULL, *graph1 = NULL;
       FILE *fp = NULL;
       _MATCH_LIST *list = NULL;

       system("clear");
       printf("\nEnter Het Group file name -->  ");
       fflush(stdout);
       fflush(stdin);
       fscanf(stdin, "%s", filename);
       ndb_clean_string(filename);

       fobjR = new CifFileObj("TEMP.CIF", WRITE_MODE);
       if (fobjR == NULL) {
            printf("Import Het Group(s) %s into component.cif failed\n", filename);
            waiting_for_continue();
            return;
       }

       fobjR->Read(filename, diags);
       if (diags && strlen(diags)) {
            printf("Read cif file %s failed\n%s\n", filename, diags);
            waiting_for_continue();
            if (fobjR) delete fobjR;
            return;
       }

       blockName = fobjR->GetBlockNames(num);
       drug = new ConnectFormat*[num];
       for (i = 0; i < num; i++) drug[i] = NULL;

       fp = fopen("compare_check_list", "w");
       for (n = 0; n < num; n++) {
            drug[n] = new ConnectFormat();
            if (Read_Chem_Comp(drug[n], fobjR, blockName[n], 0)) {
                 printf("Read Het Group %s failed\n", blockName[n]);
                 waiting_for_continue();
                 for (i = 0; i < num; i++) {
                      delete [] blockName[i];
                      if (drug[i]) delete drug[i];
                 }
                 delete [] blockName;
                 delete [] drug;
                 if (fobjR) delete fobjR;
                 return;
            }
            if (CheckFormula(drug[n], stdout, string) ||
               !CheckConnect(drug[n], stdout, string)) {
                 waiting_for_continue();
                 for (i = 0; i < num; i++) {
                      delete [] blockName[i];
                      if (drug[i]) delete drug[i];
                 }
                 delete [] blockName;
                 delete [] drug;
                 if (fobjR) delete fobjR;
                 return;
            }
            drug_tmp = Dictionary->find_drug(drug[n]->drugname());
            if (!drug_tmp) {
                 printf("Het Group %s is not in component.cif file\n",
                                 drug[n]->drugname());
                 fprintf(fp, "Het Group %s is not in component.cif file\n",
                                 drug[n]->drugname());
                 continue;
            }

            string.Copy(drug_tmp->formula());
            string1.Copy(drug[n]->formula());
            ReorderFormula(string, string2, 0);
            ReorderFormula(string1, string2, 0);
            if (string != string1) {
                 printf("Het Group %s's formula difference: New(%s) --- Exist(%s)\n",
                    drug[n]->drugname(), drug[n]->formula(), drug_tmp->formula());
                 fprintf(fp, "Het Group %s's formula difference: New(%s) --- Exist(%s)\n",
                    drug[n]->drugname(), drug[n]->formula(), drug_tmp->formula());
                 continue;
            }

            found = 0;
            graph = Connect2Graph(drug[n]);
            graph1 = Connect2Graph(drug_tmp);
            if (graph && graph1) {
                 list = graph1->find_match(*graph, n_list);
                 if (!list || n_list != drug[n]->natoms() || n_list != drug_tmp->natoms()) {
                      printf("Het Group %s is not match exist one\n", drug[n]->drugname());
                      fprintf(fp, "Het Group %s is not match exist one\n", drug[n]->drugname());
                      found = 1;
                 }
                 if (list) delete [] list;
            }
            if (graph) delete graph;
            if (graph1) delete graph1;
            if (found) continue;

            if (drug[n]->chemical_name() && drug_tmp->chemical_name() &&
                strcasecmp(drug[n]->chemical_name(), drug_tmp->chemical_name())) {
                 printf("Het Group %s's chemical_name difference: New(%s) --- Exist(%s)\n",
                    drug[n]->drugname(), drug[n]->chemical_name(), drug_tmp->chemical_name());
                 fprintf(fp, "Het Group %s's chemical_name difference: New(%s) --- Exist(%s)\n",
                    drug[n]->drugname(), drug[n]->chemical_name(), drug_tmp->chemical_name());
                 continue;
            }

            if (drug[n]->formal_charge() && drug_tmp->formal_charge() &&
                strcasecmp(drug[n]->formal_charge(), drug_tmp->formal_charge())) {
                 printf("Het Group %s's formal_charge difference: New(%s) --- Exist(%s)\n",
                    drug[n]->drugname(), drug[n]->formal_charge(), drug_tmp->formal_charge());
                 fprintf(fp, "Het Group %s's formal_charge difference: New(%s) --- Exist(%s)\n",
                    drug[n]->drugname(), drug[n]->formal_charge(), drug_tmp->formal_charge());
                 continue;
            }

            if (drug[n]->synonym() && drug_tmp->synonym() &&
                strcasecmp(drug[n]->synonym(), drug_tmp->synonym())) {
                 printf("Het Group %s's synonym difference: New(%s) --- Exist(%s)\n",
                    drug[n]->drugname(), drug[n]->synonym(), drug_tmp->synonym());
                 fprintf(fp, "Het Group %s's synonym difference: New(%s) --- Exist(%s)\n",
                    drug[n]->drugname(), drug[n]->synonym(), drug_tmp->synonym());
                 continue;
            }

            if (drug[n]->parent_residue() && drug_tmp->parent_residue() &&
                strcasecmp(drug[n]->parent_residue(), drug_tmp->parent_residue())) {
                 printf("Het Group %s's parent_residue difference: New(%s) --- Exist(%s)\n",
                    drug[n]->drugname(), drug[n]->parent_residue(), drug_tmp->parent_residue());
                 fprintf(fp, "Het Group %s's parent_residue difference: New(%s) --- Exist(%s)\n",
                    drug[n]->drugname(), drug[n]->parent_residue(), drug_tmp->parent_residue());
                 continue;
            }

            printf("Het Group %s is same\n", drug[n]->drugname());
            fprintf(fp, "Het Group %s is same\n", drug[n]->drugname());
       }
       fclose (fp);

       for (i = 0; i < num; i++) {
            delete [] blockName[i];
            if (drug[i]) delete drug[i];
       }
       delete [] blockName;
       delete [] drug;
       delete fobjR;
}

void Find_Component_Based_On_ID(Connect_Adm *Dictionary)
{
       char string[84];
       int  i, j;
       ConnectFormat *drug = NULL;

       system("clear");
       printf("\nEnter Het Group ID --> ");
       fflush(stdout);
       fflush(stdin);
       fscanf(stdin, "%s", string);
       ndb_clean_string(string);
       ndb_set_string_to_upper(string);
       if (strcmp(string, "")) {
            drug = Dictionary->find_drug(string);
            if (drug) {
                 printf("Het Group ID: %s\n", drug->drugname());
                 printf("Het Group Chemical Name: %s\n", drug->chemical_name());
                 if (drug->synonym() && strcmp(drug->synonym(), ""))
                      printf("Het Group Synonym: %s\n", drug->synonym());
                 if (drug->formula() && strcmp(drug->formula(), ""))
                      printf("Het Group Formula: %s\n", drug->formula());
                 if (drug->parent_residue() && strcmp(drug->parent_residue(), ""))
                      printf("Parent Residue: %s\n", drug->parent_residue());
                 if (drug->formal_charge() && strcmp(drug->formal_charge(), ""))
                      printf("Formal Charge: %s\n", drug->formal_charge());
                 if (drug->class_1() && strcmp(drug->class_1(), ""))
                      printf("Classification1: %s\n", drug->class_1());
                 if (drug->class_2() && strcmp(drug->class_2(), ""))
                      printf("Classification2: %s\n", drug->class_2());
                 printf("\n");

                 printf("%6s %d\n\n", drug->AtomType(), drug->typeModified());

                 printf("Atom Name     Connected Atom\n");
                 for (i = 0; i < drug->natoms(); i++) {
                      printf("  %-4s        ", drug->atoms(i)->atomname());
                      for (j = 0; j < drug->atoms(i)->nconect(); j++) {
                           printf(" %-4s", drug->atoms(i)->connectto(j));
                      }
                      printf("\n");
                 }
            } else printf("Het Group \"%s\" is not in component.cif file\n", string);
       }
       waiting_for_continue();
}

void Get_Component_From_Dictionary(Connect_Adm *Dictionary)
{
       char drug_name[84];

       system("clear");
       printf("\nPlease enter the name of Het group --> ");
       fflush(stdout);
       fflush(stdin);
       fscanf(stdin, "%s", drug_name);

       if (Get_Component_From_Dictionary(Dictionary, drug_name))
            waiting_for_continue();
}

int Get_Component_From_Dictionary(Connect_Adm *Dictionary, char *het_name)
{
       char filename[84];

       ndb_clean_string(het_name);
       ndb_set_string_to_upper(het_name);

       ConnectFormat *drug = Dictionary->find_drug(het_name);
       if (!drug) {
            printf("Can not find %s in component.cif\n", het_name);
            return 1;
       }

       CifFileObj *fobjR = new CifFileObj("./TEMP.CIF", WRITE_MODE);
       Write_Chem_Comp(drug, fobjR, 0);

       sprintf(filename, "%s.cif", het_name);
       fobjR->Write(filename);
       // fobjR->CloseFile();
       delete fobjR;
       return 0;
}

void Switch_Hold_To_Release(Connect_Adm *Dictionary, const char *filename)
{
       FILE *fp = fopen(filename, "r");
       if (fp == NULL) {
            printf("Can't open file %s\n", filename);
            return;
       }
       char line[100], date[20];
       ConnectFormat *drug = NULL;

       get_date(date);
       while (!feof(fp)) {
            fgets(line, 99, fp);
            if (feof(fp)) break;
            ndb_clean_string(line);
            drug = Dictionary->find_drug(line);
            if (drug) {
                 if (strcmp(drug->status(), "REL"))
                      drug->set_modified_date(date);
                 drug->set_status("REL");
            }
       }
       fclose (fp);
       Dictionary->WriteNdbConnect("conect_new.cif");
       Dictionary->WriteChemComp("component_new.cif", 0, "");
}

void Write_PDB_Het_Dictionary(Connect_Adm *Dictionary, const char *filename)
{
       ConnectFormat *drug = NULL;
       FILE *fp = NULL;

       fp = fopen(filename, "w");
       if (fp == NULL) {
            printf("Can't open file %s\n", filename);
            return;
       }
       drug = Dictionary->GetFirstConnect();
       while (drug) {
            if (strlen(drug->drugname()) < 4 && !strcmp(drug->status(), "REL")) {
                 Write_PDB_Conect_File(fp, drug);
            }
            drug = Dictionary->GetNextConnect();
       }
       fclose (fp);
}

void Write_All_Components_for_Client_Server(Connect_Adm *Dictionary)
{
       CifFileObj *fobjR = new CifFileObj("./TEMP.CIF", WRITE_MODE);
       ConnectFormat *drug = Dictionary->GetFirstConnect();
       while (drug) {
            if (drug->natoms() > 1 && strcmp(drug->drugname(), "BAN") &&
                strcmp(drug->drugname(), "GLX") &&
                strcmp(drug->drugname(), "ASX")) {
                 Write_Chem_Comp(drug, fobjR, 0);
            }
            drug = Dictionary->GetNextConnect();
       }
       fobjR->Write("Ligand-dict-0.cif");
       delete fobjR;
}

void Write_All_Components_for_Ligand_Server(Connect_Adm *Dictionary)
{
       char drug_name[84];
       CifFileObj *fobjR = NULL;
       ConnectFormat *drug = Dictionary->GetFirstConnect();
       while (drug) {
            if (drug->natoms() > 1 && strcmp(drug->drugname(), "BAN") &&
                strcmp(drug->drugname(), "GLX") &&
                strcmp(drug->drugname(), "ASX")) {
                 fobjR = new CifFileObj("./TEMP.CIF", WRITE_MODE);
                 Write_Chem_Comp(drug, fobjR, 0);
                 sprintf(drug_name, "%s.cif", drug->drugname());
                 fobjR->Write(drug_name);
                 delete fobjR;
            }
            drug = Dictionary->GetNextConnect();
       }
}

void Write_All_Components_Separately(Connect_Adm *Dictionary, const int flag)
{
       char drug_name[84];
       CifFileObj *fobjR = NULL;
       ConnectFormat *drug = Dictionary->GetFirstConnect();
       while (drug) {
            if (strlen(drug->drugname()) < 4 && (!flag || flag &&
               !strcmp(drug->status(), "REL"))) {
                 fobjR = new CifFileObj("./TEMP.CIF", WRITE_MODE);
                 Write_Chem_Comp(drug, fobjR, flag);
                 sprintf(drug_name, "%s.cif", drug->drugname());
                 fobjR->Write(drug_name);
                 delete fobjR;
            }
            drug = Dictionary->GetNextConnect();
       }
}

void Write_Delimited_Name_and_Formulas(Connect_Adm *Dictionary)
{
       ConnectFormat *drug = Dictionary->GetFirstConnect();
       while (drug) {
            if (strlen(drug->drugname()) < 4) {
                 printf("%s\t", drug->drugname());
                 if (drug->chemical_name() && strcmp(drug->chemical_name(), ""))
                      printf("%s", drug->chemical_name());
                 printf("\t");
                 if (drug->formula() && strcmp(drug->formula(), ""))
                      printf("%s", drug->formula());
                 printf("\t");
                 if (drug->synonym() && strcmp(drug->synonym(), ""))
                      printf("%s", drug->synonym());
                 printf("\n");
            }
            drug = Dictionary->GetNextConnect();
       }
}


static void waiting_for_continue()
{
       char buffer[10];
       char c = ' ';
       printf("\n\n [C] Continue\n");
       fflush(stdout);
       fflush(stdin);
       while (c != 'c' && c != 'C') {
            fscanf(stdin, "%s", buffer);
            ndb_clean_string(buffer);
            c = buffer[0];
       }
}

static char *Get_words(char *string, char *buffer, const char begin, const char end)
{
       *buffer = '\0';
       if (!string) return NULL;
       while (*string == ' ' && *string != '\0') string++;
       if (*string == '\0') return NULL;
       int start = 0;
       while (*string != '\0') {
            if (start) {
                 if (*string == end) {
                      string++;
                      break;
                 }
                 *buffer = *string;
                 buffer++;
            }
            if (*string == begin) start = 1;
            string++;
       }
       *buffer = '\0';
       if(*string == '\0') return NULL;
       return string;
}

static void Write_PDB_Conect_File(FILE *fp, ConnectFormat *drug)
{
       int i = 0, j = 0, k = 0, count = 2;
       char stringbuffer[10], buffer[80], *p = NULL, namebuffer[8000];
       
       fprintf(fp, "RESIDUE   %-3s    %3d\n", drug->drugname(), drug->natoms());
       for (i = 0; i < drug->natoms(); i++) {
            memset(stringbuffer, 0, 10);
            print_atom_atomName_field(stringbuffer, drug->atoms(i)->atomname(),
                       drug->atoms(i)->align_pos()); 
            fprintf(fp, "CONECT     %-4s   %2d", stringbuffer, drug->atoms(i)->nconect());
            for (j = 0; j < drug->atoms(i)->nconect(); j++) {
                 memset(stringbuffer, 0, 10);
                 for (k = 0; k < drug->natoms(); k++) {
                      if (!strcmp(drug->atoms(k)->atomname(), drug->atoms(i)->connectto(j)))
                           break;
                 }
                 if (k < drug->natoms()) {
                      print_atom_atomName_field(stringbuffer, drug->atoms(k)->atomname(),
                                 drug->atoms(k)->align_pos());
                      fprintf(fp, "%-4s ", stringbuffer);
                 }
            }
            fprintf(fp, "\n");
       }
       fprintf(fp, "END\n");

       fprintf(fp, "HET    %-3s            %3d\n", drug->drugname(), drug->natoms());
       if (drug->synonym() && strcmp(drug->synonym(), "")) {
            strcpy(namebuffer, drug->synonym());
            p = get_max_length_word(namebuffer, buffer, 55);
            fprintf(fp, "HETSYN     %-3s %s\n", drug->drugname(), buffer);
            count = 2;
            while (p) {
                 p = get_max_length_word(p, buffer, 55);
                 fprintf(fp, "HETSYN  %2d %-3s %s\n", count++, drug->drugname(), buffer);
            }
       }
       if (drug->chemical_name() && strcmp(drug->chemical_name(), "")) {
            strcpy(namebuffer, drug->chemical_name());
            p = get_max_length_word(namebuffer, buffer, 55);
            fprintf(fp, "HETNAM     %-3s %s\n", drug->drugname(), buffer);
            count = 2;
            while (p) {
                 p = get_max_length_word(p, buffer, 55);
                 fprintf(fp, "HETNAM  %2d %-3s %s\n", count++, drug->drugname(), buffer);
            }
       }
       if (drug->formal_charge() && strcmp(drug->formal_charge(), "") &&
           strcmp(drug->formal_charge(), "0"))
            fprintf(fp, "FORMUL      %-3s    %s %s\n", drug->drugname(), drug->formula(), drug->formal_charge());
       else fprintf(fp, "FORMUL      %-3s    %s\n", drug->drugname(), drug->formula());
       fprintf(fp, "\n");
}

static void print_atom_atomName_field(char *temp_line, const char *atomName, const int align)
{
       int l;

       l = strlen(atomName);
       if (l == 4 || l == 0) {
            sprintf(temp_line, "%-4s", atomName);
       } else if (align == 0) {
            if (l == 2) sprintf(temp_line, "%2s  ", atomName);
            else if (l == 3) sprintf(temp_line, "%3s ", atomName);
       } else {
            if (l == 1) sprintf(temp_line, " %s  ", atomName);
            else if (l == 2) sprintf(temp_line, " %2s ", atomName);
            else if (l == 3) sprintf(temp_line, " %3s", atomName);
       }
}

static char *get_max_length_word(char *string, char *words, const int max_length)
{
       int i, str_len, length;
       char *p;

       str_len = strlen(string);
       if (str_len <= max_length) {
            strcpy(words, string);
            return NULL;
       }

       words[0] = '\0';
       length = 0;
       for (i = 0; i < str_len; i++) {
            if (string[i] == ' ') {
                if (i >= max_length) break;
                length = i;
            // } else if (string[i] == ',' || string[i] == '-') {
            } else if (!isalnum(string[i]) && string[i] != '.' &&
                  string[i] != '(' && string[i] != '[') {
                if ((i + 1) >= max_length) break;
                length = i + 1;
            } else if (isalpha(string[i]) && (string[i+1] == '-' /* ||
                  string[i+1] == '(' || string[i+1] == '[' */ )) {
                if ((i + 1) >= max_length) break;
                length = i + 1;
            }
       }

       for (i = 0; i < length; i++) words[i] = string[i];
       words[length] = '\0';

       p = string + length;
       ndb_clean_string(p);
       if (p[0] == '\0') return NULL;
       else              return p;
}