CHAPTER 6

Input File Formats

MOLCONN .B FILE Format

The input file which contains molecule descriptions is called the .B file, which stands for BOND file. Essentially, the .B file contains connection tables in the form described below.

The input .B file in Standard MOLCONN Format contains the connection table for each of the molecules in the data set. The information for each molecule consists of three parts:

1. ID line,
2. Atom Identifiers and Connections,
3. Molecule Terminator.
1. ID line:
   a) Molecule ID : the user's sequence number (1 to 9999) for the molecule which can be used for retrieval of computed information.

   b) Molecule name : the user's name for the molecule in whatever form the user wishes; 60 character limit on the name length.

2. Atom Identities and Connections
   There is one line for each skeletal atom: Atom ID, NH, Atomic Symbol, ID s of all bonded atoms, VALD.
   a) atom ID : The sequence number of the atom in the molecular skeleton. Numbering is arbitrary but it may well be useful to conform to some standard or consistent numbering scheme.

   It should be noted that the maximum number of atoms permitted by Molconn-Z is limited by memory size and the limits put into PARAM.DAT at compilation time.

   b) NH : the number of hydrogen atoms bonded to the skeletal atom; e.g., 2 in -CH2-, 1 in -OH, 0 in Cl, 2 in -NH2.

   c) Atomic Symbol : standard atomic symbol for the atom. Recognized symbols include atoms of atomic numbers 1 - 55. Chi indexes have been tested for elements B, C, N, O, F, Si, P, S, Cl, Br, I; Kappa alpha values are established for H, B, C, N, O, F, Al, Si, P, S, Cl, Ga, Ge, As, Se, Br, Sn, Sb, Te, I.

   Special Cases:
   H may be used for a special role as in hydrogen bonding.
   Q may be used for any atom not treated by Molconn-Z. User must supply valence delta value.

   d) IDs of all bonded atoms : the IDs of all the skeletal atoms bonded to the atom.

   e) VALD (OPTIONAL) : an alternate value for dv may be supplied here by the user; used when no standard value is available in Molconn-Z. The user supplied value must contain a decimal point and is limited to a maximum of five decimal places, e.g.: 3,0,Se,2,4,0.22222

   The general nonempirical relation may be a guide: dv = (Zv - h)/(Z - Zv -1).

3. Molecule Termination

   Each molecule is terminated with a '-1' on a separate line.

   NOTE: Each quantity described above is separated from the next by either a comma or a blank (field delimiter). The user can specify either of the field delimiters in the OPTION section of the program by referring to Option 2 in the first submenu. The standard option is a comma.

4. File Termination

   The signal to the Molconn-Z program that the end of the .B file has been reached is a '-1'. In general, the .B file will contain two consecutive lines at the end with a '-1'; one for the end of the last molecule and one for the end-of-file signal. See the example .B file, SAMPLE.B.

The definitions given above are illustrated by examples below. Further, the file SAMPLE.B (supplied with the Molconn-Z software) also contains many more examples. See the listing of this file at the end of this chapter.

---

Examples for Standard Molconn-Z Format

Example 1: Serotonin



2, Serotonin
1,0,C,2,9,10
2,1,C,1,3
3,1,N,2,4
4,0,C,3,5,9
5,1,C,4,6
6,1,C,5,7
7,0,C,6,8,13
8,1,C,7,9
9,0,C,1,4,8
10,2,C,1,11
11,2,C,10,12
12,2,N,11
13,1,O,7
-1

Example 2: 4-Chlorophenol



1, 4-Chlorophenol
1,0,C,2,6,7
2,1,1,3
3,1,C,2,4
4,0,C,3,5,8
5,1,C,4,6                                
6,1,C,1,5
7,1,O,1
8,0,Cl,4
-1

Example 3: 2,2-Dimethyl-5-chloro-pentane-4-one

3, 2,2-Dimethyl-5-chloro-pentane-4-one
1,3,C,2
2,0,C,1,3,7,8
3,2,C,2,4
4,0,C,3,5,9
5,2,C,4,6
6,0,Cl,5
7,3,C,2
8,3,C,2
9,0,O,4
-1

---

Use of SMILES Code in Input Format

Molconn-Z has several options for use of input file format. The input option is selected as item 1 in the MENU section of the program. To use the SMILES code, the user selects 'S' from the Main Menu in option 1.

SMILES code was developed by David Weininger (D. Weininger, J. Chem. Inf. Comput. Sci., 28, 31-36, 1988) to provide a string code for the input of molecular structure. The user is referred to this reference and subsequent papers for the description of the SMILES code and techniques for creation of SMILES code for molecular structures. The following two structures illustrate the application of SMILES code. Essentially, the chemical graph is reduced to a tree (noncyclic) graph by removing one bond for each ring; the atoms between which the bond was broken are labeled with a number. Branches are enclosed in parentheses.

---

Examples

The following is the contents of the example input file which illustrates SMILES code, SMILES.B, from the Molconn-Z software package.

The File SMILES.B as Supplied in Molconn-Z Software:

1, 6-Hydroxy-1,4-hexadiene
C=CCC=CCO
2, Triethylamine
CCN(CC)CC
3, Isobutyric Acid
CC(C)C(=O)O
4, 3-Propyl-4-isopropyl-1-heptene
C=CC(CCC)C(C(C)C)CCC
5, Benzene
c1ccccc1
6, 3-Bromo,methycyclohex-1-ene
CC1=CC(Br)CCC1
7, Cubane
C12C3C4C1C5C4C3C25
8, Tetramethyl silane
C[Si](C)(C)C
9, Morphine
O1C2C(O)C=CC3C2(C4)c5c1c(O)ccc5CC3N(C)C4
-1

Note that the '-1' file terminator is used as the last entry in the file.

Three extensions have been made to SMILES code interpretation for Molconn-Z version 3.0+.

1. Ring closure numbers have been extended beyond the range 0 to 9. For higher numbers, a % sign must be included. For example, for cyclobutane, if one wished, the following string can be used: C%11CCC%11. This additional feature permits more than 10 rings per structure.

2. Ring closure numbers may now be reused within the same string. The SMILES interpreter will, of course, assume that the second occurrence of a given digit must be paired with the first occurrence of that digit. For example, biphenyl could be written as follows: c1ccccc1c2ccccc2 or as c1ccccc1c1ccccc1. The string c1ccccc2c1ccccc2 would correspond to an entirely different structure.

3. The length of the SMILES string allowed for input has been increased to 256.

---

Molecule Files from CHEM-X of Chemical Design Ltd.

Molconn-Z has several options for use of input file format. The input option is selected as item 1 in the MENU section of the program. To use files in the CHEM-X format, the user selects 'X' from the Main Menu in option 1.

The use of molecule files produced by Chem-X is very easily done. The user first produces the desired molecule files by using Chem-X in its usual manner. Each molecule file is produced with a unique name, usually closely associated with the name of the molecule. These molecule file names are entered into the .B file rather than the connection table information required by the standard Molconn-Z format. The molecule file names become pointers to the actual connection table information in the Chem-X molecule files. It is most helpful to have all the Chem-X molecule files in the directory in which the user is working.

For example, suppose the user has produced Chem-X files for the following molecules: acetic acid and benzoic acid with the following file names: ACETICAC.CSS, CLBENZCA.CSS (Note: VAX style notation is used here and the suffix CSSR (shortened to CSS here) is simply an acronym for Cambridge Structure Search Routine and not necessary for general use.) Then, the Molconn-Z .B file, let's call it CHX.B, will have the following form:

The File CHX.B as Supplied in Molconn-Z Software:

1, ACETICAC.CSS
2, CLBENZCA.CSS
3, ETHANOL.CSS
-1

It is of the utmost importance that the file names in the .B file be exactly as they appear in the directory listing. The usual '-1' file terminator is used.

The test input file CHX.B is supplied with the Molconn-Z software along with the appropriate Chem-X molecule files ACETICAC.CSS, CLBENZCA.CSS, and ETHANOL.CSS.

Chem-X is developed and distributed by
Chemical Design, Ltd.
Oxford, England

---

Molecule Files from ChemLab and MicroChem(TM)

THIS FILE FORMAT IS NO LONGER SUPPORTED BY HALL ASSOCIATES. IF A USER DESIRES THIS FORMAT, CONTACT HALL ASSOCIATES FOR A CUSTOMIZED VERSION OF MOLCONN-Z.

MicroChem(TM) is a trademark of Intersoft, Inc.
282 East Woodland Rd.
Lake Forest, IL 60045

---

Molecule Files from ChemDraw File Formats

Molconn-Z has several options for use of input file format. The input option is selected as item 1 in the MENU section of the program. For use of files from ChemDraw, select 'D' in option 1 in the Main Menu.

The use of molecule files produced by ChemDraw is very easily done. The user first produces the desired molecule files by using ChemDraw in its usual manner. Each molecule file is produced with a unique name, usually closely associated with the name of the molecule. These molecule file names are entered into the .B file rather than the connection table information required by the standard Molconn-Z format. The molecule file names become pointers to the actual connection table information in the ChemDraw molecule files. It is most helpful to have all the ChemDraw molecule files in the directory in which the user is working. For example, suppose the user has produced ChemDraw files for the following molecules : pyridine and propanoic acid, with the following file names: PYRIDINE.TBL and PROP_ACD.TBL. (Note: VAX style notation is used here.) Then, the Molconn-Z .B file, let's call it CDRAW.B, will have the following form:

The File CDRAW.B as Supplied in Molconn-Z Software:

1, PYRIDINE.TBL
2, PROP_ACD.TBL
3, PYRIDIN0.TBL
4, 4CLBIPHE.TBL
-1

It is of the utmost importance that the file names in the .B file be exactly as they appear in the directory listing. The usual '-1' file terminator is used.

The test input file CDRAW.B is supplied with the Molconn-Z software along with the ChemDraw molecule files PYRIDINE.TBL , PROP_ACD.TBL, PYRIDIN0.TBL , and 4CLBIPHE.TBL.

ChemDraw is a trademark of Cambridge Scientific Computing, Inc.
875 Massachusetts Ave.
Cambridge, MA 02139

---

Molecule Files from MDL Information Systems, Inc. Molfiles

Molconn-Z has several options for use of input file format. The input option is selected as item 1 in the MENU section of the program. The user selects 'M' for use of files in the Molfile format from MDL Information Systems, Inc. in option 1 in the Main Menu. For a complete description of the Molfile, see A. Dalby, J. G. Nourse, et al., J. Chem. Inf. Comput. Sci., 32, 244-255 (1992).

The use of molecule files in the Molfile format produced by MDL software is easily done. The user first produces the desired molecule files by using MDL software in its usual manner. Each molecule file is produced with a unique name, usually closely associated with the name of the molecule. These molecule file names are entered into the .B file rather than the connection table information required by the standard Molconn-Z format. The molecule file names become pointers to the actual connection table information in the Molfile. It is most helpful to have all the Molfiles in the directory in which the user is working.,p> For example, suppose the user has produced Molfiles with the following file names: PHENOL.MOL, CLPHENOL.MOL, CNPHENOL.MOL, NNPHENOL.MOL, and SNPHENOL.MOL Then, the Molconn-Z .B file, let's call it MDL.B, will have the following form:

The File MDL.B as Supplied in Molconn-Z Software:

1, PHENOL.MOL
2, 4CLPHENOL.MOL
3, CNPHENOL.MOL
4, NNPHENOL.MOL
5, SNPHENOL.MOL
-1

It is of the utmost importance that the file names in the .B file be exactly as they appear in the directory listing. The usual '-1' file terminator is used.

The test input file MDL.B is supplied with the Molconn-Z software along with the MDL molecule files PHENOL.MOL and 4CLPHENOL.MOL.

MOL file format is licensed by MDL Information Systems, Inc.
San Leandro, CA

---

SDFiles from MDL Information Systems, Inc., using Molfiles

MDL also supports an additional type of file format which includes structure data in the form of the Molfile. This SDFile also includes provision for an unspecified number of records which contain data of various types for each molecule. The data may be numerical or alphabetic. Select 'F' in Menu option 1 for SDFile input format.

This Structure Data file (SDFile) is carefully described in A. Dalby, J. G. Nourse, et al., J. Chem. Inf. Comput. Sci., 32, 244-255 (1992).

The use of the SDFile format produced by MDL software is easily done. The user first produces the desired molecule files by using MDL software in its usual manner. These molecule files are incorporated into the .B file along with the data lines desired by the used, following each Molfile. The record separating the Molfile from the data records contains 'M END'. See the example below and the reference given above. The information for each molecule is terminated by a blank record followed by a record containing $$$$. The whole SDFile is terminated with a blank record.

For example, suppose the user has produced an SDFile for the following molecules: phenol and 4-chloro-2-nitrophenol. Let's call it SDF.B. It will have the following form:

The File SDF.B as Supplied in Molconn-Z Software:

PHENOL
JFMACCS 8302248414282D 1   0.00213     0.00000     0     JF
FOR PROGRAM MOLCONN2
  7  7  0  0  0
    0.7943   -0.2132    0.0000 C   0  0  0  0  0
    0.0023   -1.5022    0.0000 C   0  0  0  0  0
   -1.5284   -1.4655    0.0000 C   0  0  0  0  0
   -2.2648   -0.1072    0.0000 C   0  0  0  0  0
   -1.4690    1.1987    0.0000 C   0  0  0  0  0
    0.0565    1.1609    0.0000 C   0  0  0  0  0
    2.3413   -0.2625    0.0000 O   0  0  0  0  0
  1  2  2  0  0  0
  2  3  1  0  0  0
  3  4  2  0  0  0
  4  5  1  0  0  0
  5  6  2  0  0  0
  6  1  1  0  0  0
  1  7  1  0  0  0
M END
> 25 <BOILING POINT>
182.0

> 25 <MELTING POINT>
40.0 - 42.0

> 25 <ALTERNATE NAME>
Hydroxybenzene

> 25 <DATE>
10-02-92

$$$$
2-Chloro-4-nitro PHENOL
XXMACCS 8302248414282D 1   0.00213     0.00000     0     JF
FOR PROGRAM MOLCONN2
 11 11  0  0  0
    0.7943   -0.2132    0.0000 C   0  0  0  0  0
    0.0023   -1.5022    0.0000 C   0  0  0  0  0
   -1.5284   -1.4655    0.0000 C   0  0  0  0  0
   -2.2648   -0.1072    0.0000 C   0  0  0  0  0
   -1.4690    1.1987    0.0000 C   0  0  0  0  0
    0.0565    1.1609    0.0000 C   0  0  0  0  0
    2.3413   -0.2625    0.0000 O   0  0  0  0  0
    1.0       1.0       0.0000 Cl  0  0  0  0  0
    2.0       2.0       0.0000 N   0  0  0  0  0
    3.0       3.0       0.0000 O   0  0  0  0  0
    4.0       4.0       0.0000 O   0  0  0  0  0
  1  2  2  0  0  0
  2  3  1  0  0  0
  3  4  2  0  0  0
  4  5  1  0  0  0
  5  6  2  0  0  0
  6  1  1  0  0  0
  1  7  1  0  0  0
  2  8  1  0  0  0
  4  9  1  0  0  0
  9 10  2  0  0  0
  9 11  2  0  0  0
M END
> 25 <MELTING POINT>
85.0 - 87.0

> 25 <PHYSIOLOGICAL>
IRRITANT

$$$$

(Note "blank" record to terminate file!!!)

The test input file SDF.B is supplied with the Molconn-Z software.

Molfile format is licensed by MDL Information Systems, Inc.
San Leandro, CA

---

SMILES Strings using the Daylight Toolkit Format (unix only)

The SGI and (potentially) some other UNIX versions of standalone Molconn-Z have the added capability of reading and decoding SMILES files using the Daylight Toolkit SMILES interpreter instead of the built-in Molconn-Z SMILES interpreter. This is an optional feature that requires additional licensing from eduSoft, LC/Hall Associates and a run-time SMILES Toolkit license from Daylight Chemical Information Systems, Inc. Each record of the Daylight SMILES files, which are generally named with the .smi extension, is simply a SMILES String followed by the Molecule Name (space delimited). There is no file termination code. This file format matches what is supported by the Daylight database software and be a useful option for some sites that have large databases already encoded in this way. The other potential advantage is that the Daylight Toolkit is the defacto standard for interpretation of SMILES codes; while we have done no head-to-head comparisons and can cite no specific examples, we believe that the Daylight methodology is probably more robust for this function than the built-in Molconn-Z decoder and would recommend, for those who plan to work with SMILES on unix computers, to consider licensing this option.

The File smallmol.smi as Supplied in Unix Versions of Molconn-Z Software:

c1ccccc1 benzene
C(Cl)(Cl)Cl chloroform
CC ethane
C1CCCCC1 cyclohexane
CC(C)(C)O tbutanol
c1cccc2ccccc12 napthalene
C1(O)C(O)C(O)C(CO)OC1OC(C(CO)O)C(O)C(O)C(=O)O maltobionic_acid
c1ccccc1CC(N)C amphetamine
c1cc(C)ccc1Cc(cc2)ccc2C di_p_tolyl_methane

---

Molecule Files from User Supplied File Formats

Molconn-Z has several options for use of input file format. The input option is selected as item 1 in the MENU section of the program. This option is selected as 'U' in option 1 in the Main Menu section of the program.

The Molconn-Z program is currently set up to accept input files in several formats. If the user has a different file format for molecules, the user may request the object code for Molconn-Z with an appropriate entry point subroutine (USERFIL) that can be end-user coded to accept these files as input. Alternatively, the user may contact Hall Associates for the possibility of a customized version of USRFIL.

1, Propanol     
1,3,C,2 
2,2,C,1,3                                                                       
3,2,C,2,4                
4,1,O,3    
-1
 2, 2-Propanol                          
1,3,C,2                                                                         
2,1,C,1,3,4                                                                     
3,1,O,2                                                                         
4,3,C,2                                                                         
-1
 3, Aniline
1,0,C,2,6,7                                                                     
2,1,C,1,3                                                                       
3,1,C,2,4                                                                       
4,1,C,3,5                                                                       
5,1,C,4,6                                                                       
6,1,C,5,1                                                                       
7,2,N,1                                                                         
-1
 4, Benzyl alcohol                       
1,0,C,2,6,7                                                                     
2,1,C,1,3                                                                       
3,1,C,2,4                                                                       
4,1,C,3,5                                                                       
5,1,C,4,6                                                                       
6,1,C,5,1                                                                       
7,2,C,1,8                                                                       
8,1,O,7                                                                         
-1
5, 3-Bromo phenol
1,0,C,2,6,7
2,1,C,1,3
3,0,C,2,4,8
4,1,C,3,5
5,1,C,4,6
6,1,C,1,5
7,1,O,1
8,0,Br,3
-1
 6, Benzimidazole                          
1,1,N,2,5                                                                       
2,1,C,1,3                                                                       
3,0,N,2,4                                                                       
4,0,C,3,5,9                                                                     
5,0,C,4,1,6                                                                     
6,1,C,5,7                                                                       
7,1,C,6,8                                                                       
8,1,C,7,9                                                                       
9,1,C,8,4                                                                       
-1
 7, Adamantyl amine
1,0,C,2,8,9,11
2,2,C,1,3
3,1,C,2,4,10
4,2,C,3,5
5,1,C,4,6,9
6,2,C,5,7
7,1,C,6,8,10
8,2,C,1,7
9,2,C,1,5
10,2,C,3,7
11,2,N,1
-1
 8, Ephedrine                              
1,0,C,2,6,7                                                                     
2,1,C,1,3                                                                       
3,1,C,2,4                                                                       
4,1,C,3,5                                                                       
5,1,C,4,6                                                                       
6,1,C,5,1                                                                       
7,1,C,1,8,9                                                                     
8,1,O,7                                                                         
9,1,C,7,10,11                                                                   
10,3,C,9                                                                        
11,1,N,9,12                                                                     
12,3,C,11                                                                       
-1
9, 4,4'-Dichloro biphenyl
1,0,C,2,6,7
2,1,C,1,3
3,1,C,2,4
4,0,C,3,5,8
5,1,C,4,6
6,1,C,5,1
7,0,Cl,1
8,0,C,4,9,13
9,1,C,8,10
10,1,C,9,11
11,0,C,10,12,14
12,1,C,11,13
13,1,C,8,12
14,0,Cl,11
-1
-1