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1. >ATOMS M

The record item provides the information about atoms contained in query. M is the number of atoms(M<=125). One data line is for one atom.

format:

atom_id atom_type(impH)

fields:

atom_id(integer)= id number of atom .

atom_type(string)= symbol of actual atom , such as C, O, N or Cl.

or symbol of such a point as

*(Any atom type), Cn(Chain),

Hr(Hbond acceptor), Hd(Hbond donor),

Pc(Positive charge center), Nc(Negative charge center),

Hy(Hydrophobe), Pi(Aromatic ring center),

Da(N or O), Db(N, O or S) or Dc(O or S).

if atom_type is Hy, two integers must follow representing the min number and max
number of atoms in the hydrophobe, respectively. The default values are 3 and 50

if atom_type is Hr or Hd, the type(string) of main atom in Hbond acceptor or Hbond
donor must follow. The default is *(any atom type).

impH(string)=implicit hydrogen atom only if implicit hydrogen of atom
must be matched.

example:

>ATOMS 4

1 N

2 CH2

3 Hy 3 6

4 Hr N

In this example, there are four atoms in query , the first atom is N atom, the second one is C atom with two hydrogens, the third one is a hydrophobe with the number of atoms between 3 and 6, and the forth one is a Hbond acceptor which main atom is N atom.

2. >CENTROIDS M

The record item provides the information about centroids in query, if defined. M is the number of centriods(M<= 10). One data line is for one centroid.

format:

CR_id atom_id atom_id ... atom_id

fields:

CR_id (string)= id number of centroid

atom_id (integer)= id number of component atom of centroid

example:

>CENTROINDS 2

CR01 1 2 4 5 7

CR02 3 5 7 6

In this example, two centroids are defined in query, the first one CR01 consists of atom 1, 2 , 4, 5and 7 and the second one CR02 consists of atom 3, 5, 7, and 6.

3. >PLANES M

The record item provides the information about planes in query, if defined. M is the number of planes(M<= 5). One data line is for one plane.

format:

plane_id atom_id atom_id ... atom_id

fields:

plane_id(string) = id number of plane.

atom_id (integer)= id number of component atom of plane

example:

>PLANES 2

PL01 1 2 7

PL02 3 5 6

In this example, two planes are defined in query, the first one PL01 is determined by atom 1, 2 and 7, the second one PL02 is determined by atom 3, 5 and 6.

4. >LONE PAIRS M

If the direction of lone pair of an atom is constrained in query, the atom is specified in this record item. M is the number of such atoms(M<= 5). One data line is for one atoms.

format:

lone-pair_id atom_id

fields:

lone-pair_id (string) = id number of lone pair

atom_id (integer)= id number of atom with constrained lone pair direction

example:

>LONE PAIRS 1

LP01 4

In this example, lone pair direction of one atom is constrained, the id number of the atom is 4. The id number of the lone pair is LP01

5. >BONDS M

The record item provides the information about bonds in query. M is the number of bonds(M<= 125). One data line is for one bond.

format:

origin_atom_id target_atom_id bond_type

fields:

origin_atom_id (integer)= id number of the atom on one end of bond.

target_atom_id (integer)= id number of the atom on the other end of bond

bond_type (integer)= bond type, 1 for single bond, 2 for double bond, 3 for
triple bond.

example:

>BONDS 3

1 2 1

1 3 1

2 4 2

In this example, there are three bonds in query. The first bond is a single bond connecting atom 1 and 2. The second one is a single bond connecting atom 1 and 3. The third one is a double bond connecting atom 2 and 4

6. >DISCONS M

The record item provides the information of disconnectivity of pharmacophore query. M is the number of disconnected fragments in query(M<= 6). One data line is for one disconnected fragment.

format:

atom_id

fields:

atom_id (integer)= id number of any atom in disconnected fragment.

example:

>DISCONS 2

1

4

In this example, The query consists of two disconnected fragments, atom 1 is the starting atom of the first fragment and atom 4 is the starting atom of the second fragment.

7. >DISTANCE CONSTRAINTS M

The record item provides the information about distance constraints in query. M is the number of distance constraints(M<= 10). One data line is for one constraint.

format:

from_point_id to_point_id dis error_d

fields:

from_point_id (integer or string) = id number of atom(or centroid) on
one end of the distance.

to_point_id (integer or string) = id number of atom(or centroid) on the
other end of distance

dis (float) = distance value(Þ )

error_d(float) = allowed tolerance(Þ )

example:

>DISTANCE CONSTRAINTS 3

1 2 3.4 0.5

2 3 5.4 0.6

CR01 3 6.5 1.0

In this example, there are three distance constraints in query. The distance between atom 1 and atom 2 is 3.4Þ and the tolerance is 0.5Þ . The distance between atom 2 and atom 3 is 5.4Þ and the tolerance is 0.6Þ . The distance between centroid CR01 and atom 3 is 6.5Þ and the tolerance is 1.0Þ .

8. >ANGLE CONSTRAINTS M

The record item provides the information about 3-point angle constraints in query. M is the number of angle constraints(M£ 10). One data line is for one constraint.

format:

left_point_id cent_point_id right_point_id ang error_ang

fields:

left_point_id (integer or string) = id number of left atom(centroid,
or lone pair) used to define a 3-point angle

cent_point_id (integer or string) = id number of the vertex atom( centroid)
used to define a 3-point angle

right_point_id (integer or string) = id number of right atom(centroid)
used to define a 3-point angle

ang (float) = angle value(degree)

error_ang(float) = allowed tolerance(degree)

note: If the left(or right) point of a 3-point angle is lone pair, the vertex must be the atom
which the lone pair belongs to.

example:

>ANGLE CONSTRAINTS 3

1 2 3 60.0 5.0

1 CR01 3 50.0 10.0

LP01 2 3 35.0 5.0

In this example, there are three 3-point angle constraints in query. The angle <1-2-3 is 60° and the tolerance is 5° . The angle < 1-CR01-3 is 50° and the tolerance is 10° . The angle < LP01-2-3 is 35° and the tolerance is 5° and LP01 is the lone pair of atom 2.

9. >PLANE_LINE ANGLE CONSTRAINTS M

The record item provides the information about angle constraints between the normal line of a plane and a line defined by two points in query. M is the number of such angle constraints(M<= 5). One data line is for one constraint.

format:

plane_id from_point_id to_point_id g error_g

fields:

plane_id (string) = id number of plane
from_point_id (integer or string) = id number of one atom(centroid,
or lone pair) used to define a line
to_point_id (integer or string) = id number of the other atom( centroid)
used to define a line

g (float) = angle value(degree)

error_g(float) = allowed tolerance(degree)

example:

>PLANE_LINE ANGLE CONSTRAINTS 2

PL01 2 3 60.0 5.0

PL01 CR01 3 50.0 10.0

In this example, there are two plane_line angle constraints in query. The angle between the normal line of plane PL01 and the line of atom 2 and atom 3 is 60° and the tolerance is 5° . The angle between the normal line of plane PL01 and the line centroid CR01 and atom 3 is 50° and the tolerance is 10° .

10. >PLANE_PLANE ANGLE CONSTRAINTS M

The record item provides the information about angle constraints between two planes in query. M is the number of such angle constraints(M<= 5). One data line is for one constraint.

format:

plane_id plane_id p error_p

fields:

plane_id (string) = id number of one plane
plane_id (string) = id number of the other plane

p (float) = angle value(degree)

error_p(float) = allowed tolerance(degree)

example:

>PLANE_PLANE ANGLE CONSTRAINTS 1

PL01 PL02 60.0 5.0

In this example, there is one plane_plane angle constraint in query. The angle between plane PL01 and plane PL02 is 60° and the tolerance is 5° .

11. >DIHEDRAL ANGLE CONSTRAINTS M

The record item provides the information about dihedral angle constraints in query. M is the number of dihedral angle constraints(M<= 10). One data line is for one constraint.

format:

point1_id point2_id point3_id point3_id dih error_dih

fields:

point1_id (integer or string) = id number of first atom(centroid or lone pair)

point2_id (integer or string) = id number of second atom(centroid)

point3_id (integer or string) = id number of third atom(centroid or lone pair)

point4_id (integer or string) = id number of forth atom(centroid)

dih (float) = angle value(degree)

error_dih(float) = allowed tolerance(degree)

example:

>DIHEDRAL ANGLE CONSTRAINTS 2

1 2 3 4 60.0 5.0

CR01 2 4 5 50.0 10.0

In this example, there are two dihedral angle constraints in query. The dihedral angle of atom 1-> 2- 3-> 4 is 60° and the tolerance is 5° . The dihedral angle of CR01-> 2- 3-> 4 is 50° and the tolerance is 10° .

12. >PLANE SIDE CONSTRAINTS M

The record item specifies that two points lie on the same side or opposite side of a plane defined in query. M is the number of the plane side constraints(M<= 5). One data line is for one constraint.

format:

plane_id point1_id || (&) point2_id

fields:

plane_id (string) = id number of plane
point1_id (integer or string) = id number of one atom(centroid)
point1_id (integer or string) = id number of the other atom(centroid)

& = same side

|| = opposite side

example:

>PLANE SIDE CONSTRAINTS 2

PL01 1 || 3

PL02 1 & 4

In this example, there are two plane side constraints in query. Atom 1 and atom 2 lie on the opposite side of plane PL01. Atom 1 and atom 4 lie on the same side of plane PL02.

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